Objective To explore the effect of periodontal basic treatment combined with invisible orthodontics treatment on the periodontal health level of patients with malocclusion and chronic periodontitis. Methods A total of 60 patients with malocclusion complicated with chronic periodontitis admitted to our hospital from January 2021 to September 2023 were selected as the research subjects. According to different treatment plans, they were divided into the control group and the observation group, with 30 patients in each group. The control group received basic periodontal treatment combined with fixed orthodontics treatment, and the observation group received periodontal basic treatment combined with invisible orthodontics treatment. The orthodontic treatment effect, periodontal indexes and complications were compared between the two groups. Results The total effective rate of orthodontic treatment in the observation group was 90.00%, which was higher than 86.67% in the control group, but the difference was not statistically significant (P >0.05). After treatment, the probing depth, clinical attachment level, plaque index and sulcus bleeding index in the observation group were all better than those in the control group, and the differences were statistically significant (P <0.05). The incidence of complications in the observation group was 6.67%, which was lower than 30.00% in the control group, and the difference was statistically significant (P <0.05). Conclusion Periodontal basic treatment combined with invisible orthodontics treatment for patients with malocclusion and chronic periodontitis has an ideal effect. It can achieve an ideal orthodontic treatment effect, promote the periodontal health of patients, and is safe and reliable.